Something I have noticed is that SSD's speed up Malwarebyte scans by an insane amount (assuming you only scan the SSD). A full scan of 300k+ objects only take like 15 minutes.
Progress Report:
Malwarebytes Anti-Malware (PRO) 1.75.0.1300
www.malwarebytes.org
Database version: v2014.04.16.04
Windows 7 Service Pack 1 x64 NTFS
Internet Explorer 8.0.7601.17514
X:: XXXXXXXXXXX [administrator]
Protection: Enabled
4/16/2014 9:53:13 AM
mbam-log-2014-04-16 (09-53-13).txt
Scan type: Full scan (C:\|D:\|)
Scan options enabled: Memory | Startup | Registry | File System | Heuristics/Extra | Heuristics/Shuriken | PUP | PUM
Scan options disabled: P2P
Objects scanned: 338273
Time elapsed: 13 minute(s), 24 second(s)
Memory Processes Detected: 0
(No malicious items detected)
Memory Modules Detected: 0
(No malicious items detected)
Registry Keys Detected: 0
(No malicious items detected)
Registry Values Detected: 0
(No malicious items detected)
Registry Data Items Detected: 0
(No malicious items detected)
Folders Detected: 0
(No malicious items detected)
Files Detected: 0
(No malicious items detected)
(end)
My suggestion for when things get this bad is to just reload the whole OS (probably easier than trying to save it). After re-install run HousecallTrend Micro HouseCall (this scan normally takes me hours, and on some computers I have seen it take over 24 hours). Then run Malwarebytes.
At least, that's what I do when I get into a situation where literally every file seems to be infected. Also, 21k seems like way too many.